Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__PV4:5208462 Length = 378 Score = 226 bits (577), Expect = 6e-64 Identities = 115/237 (48%), Positives = 157/237 (66%), Gaps = 2/237 (0%) Query: 17 DKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKD 76 D AVD + + I GE L+G SG GKST LRMLAG E G I + +D+T +PP + Sbjct: 32 DVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYLDGQDITDMPPYE 91 Query: 77 RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKAL 136 R I M+FQ+YAL+PHMTVA N+ F LK +PKAEI Q+V+E K++ + Y RKP L Sbjct: 92 RPINMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKEMLKLVHMEPYAKRKPNQL 151 Query: 137 SGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQ 196 SGGQRQRVA+ R++ + P++ L+DEP+ LD KLR + ++ + +G+T V VTHDQ Sbjct: 152 SGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVDILEAVGVTCVMVTHDQ 211 Query: 197 VEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGV 253 EAMTM +R+A++ DG + Q SP ++Y+ PAN VA FIGS +NL E I + V Sbjct: 212 EEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFIGS--VNLFEGDIVEDEV 266 Lambda K H 0.317 0.135 0.379 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 356 Number of extensions: 17 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 377 Length of database: 378 Length adjustment: 30 Effective length of query: 347 Effective length of database: 348 Effective search space: 120756 Effective search space used: 120756 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory